Editing particles to remove troublesome boid instances
I don't think you can actually delete the boid or its path but you can move it out of the way so that it isn't visible as part of the simulation.

This can be achieved using the Particle Edit mode after you have Baked your simulation. Note that this must be baked into memory rather than a disk file - since the Particle Edit can only operate on particle systems held in memory.

In Particle select mode, choose the 'Point' select mode to allow you to manipulate all points in the particle system.



You might also find it useful to increase the Draw Path Steps in the Toolshelf (T) to make the visible paths more detail (makes it more smoothed). Also, disable the Keep Root setting so that you can move the whole path without it being joined to the emitter (used below).



Select one of the points on the path you want to 'move'



Then hit L to select 'Linked' - ie, select the whole path.



You can now 'grab' (G) the path and, since it's disconnected from its 'root' (the toolshelf checkbox you unchecked earlier) you can move it away from the emitter.



To make the selected boid even easier to 'hide' you can scale the path to zero to make it occupy a single point with S0Enter.